xsact-1.6: Cluster EST sequences Contents Index

Pairs

Synopsis

data Match = Match !Suffix !Suffix data SMPair = SMPair !Dir !EST !EST !Int [Block] class Pair a n | a -> n where score :: a -> Int ests :: a -> (n, n) pairs :: Bool -> [Match] -> [SMPair] matches :: [[Suffix]] -> [Match] sort_pure :: [Match] -> [Match] sort_io :: [EST] -> String -> [Match] -> IO [Match] mpairs :: Bool -> [Match] -> [(Maybe MPair, Maybe MPair)] elim_bs :: SMPair -> SMPair psort :: [SMPair] -> [SMPair] collect :: Bool -> [Match] -> [([Match], [Match])] blocks :: ([Match], [Match]) -> (Maybe MPair, Maybe MPair) showmatch :: Match -> String direction :: SMPair -> Bool prefixes :: Int -> [[Gene]] merge_suffix_lists :: [EST] -> Int -> String -> IO [Match] show_header :: SMPair -> String show_regs :: SMPair -> String

Documentation

data Match

Constructors Match !Suffix !Suffix Instances Show Match Pair Match EST

data SMPair

Constructors SMPair !Dir !EST !EST !Int [Block] Instances Show SMPair Pair SMPair EST

class Pair a n | a -> n where

Methods score :: a -> Int ests :: a -> (n, n) Instances Pair MPair EST Pair Match EST Pair Match EST Pair SMPair EST Pair SMPair EST

pairs :: Bool -> [Match] -> [SMPair]

Construct scored pairs from {tt Match}es.

matches :: [[Suffix]] -> [Match]

sort_pure :: [Match] -> [Match]

sort_io :: [EST] -> String -> [Match] -> IO [Match]

mpairs :: Bool -> [Match] -> [(Maybe MPair, Maybe MPair)]

elim_bs :: SMPair -> SMPair

psort :: [SMPair] -> [SMPair]

sort pairs by score

collect :: Bool -> [Match] -> [([Match], [Match])]

blocks :: ([Match], [Match]) -> (Maybe MPair, Maybe MPair)

showmatch :: Match -> String

direction :: SMPair -> Bool

prefixes :: Int -> [[Gene]]

calculate prefixes (also used in Xsact)

merge_suffix_lists :: [EST] -> Int -> String -> IO [Match]

show_header :: SMPair -> String

show_regs :: SMPair -> String

Produced by Haddock version 2.1.0